I wonder if this is due to how a cluster is configured to function internally.
Tell us more about the cluster, is it one of those ‘fancy pants’ high availability, auto backup heart beat things, or is it more a traditional multi server (master slave style) setup.
Either way you may need to disconnect the servers from one another and delete the offending files / directories either via dove or or via the os (although reading your original email it sounds like you are already attempting this).
If you have a fancy cluster this may actually be more difficult than it sounds and have interesting (unwanted) side effects, also the underlying database (if you are storing emails that way) may have a method to remove data
I assume you are keeping back up copies of all those emails somewhere, just in case you need them in the future.
See this wiki article to better understand what I mean by the ‘fancy pants’ clusters :
They sound very cool, but I suspect are overkill for a mail server, unless your database is already inside one then it would make sense I guess.
I just use the cluster/replication functionality integrated into dovecot, nothing more. There is no database involved. I use LDAP for the authentication. The mails are stored locally on each server and replicated with the replication feature of dovecot.